Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae -- Kadirvelraj et al. 103 (21): 8149 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Kadirvelraj et al. 10.1073/pnas.0602815103.

Supporting Information

Files in this Data Supplement:

Supporting Table 3
Supporting Table 4
Supporting Movie 1
Supporting Table 5
Supporting Table 6
Supporting Figure 5
Supporting Figure 6
Supporting Figure 7

Fig. 5.
A superimposition of the average CPS conformations present in the immune complex (black) and free in solution (gray).

Fig. 6.
Electrostatic potential surface of the binding site of Fv. The molecular surfaces are colored according to electrostatic potential. Positive potential is shown in blue, and negative potential is in red; the contouring value of the potential is in kT/e. The image was drawn using PYMOL Molecular Graphics System (DeLano Scientific, San Carlos, CA).

Fig. 7.
Superimposition of the ribbon structures of the backbones of V_H1A7R (blue) and V_H1NSN (red) with the H3 loops highlighted in orange.

Supporting Movie 1

Movie 1.
MD simulation of model immune complex between Fv1B1 and CPS from GBSIII (L ® H threading).

Table 3. Predicted H-bond occupancies, distances, and ring-stacking interactions between Fv 1B1 and the GBSIII CPS (L → H threading)

H-bond^*
CPS atom	Fv atom	Occupancy, %	Distance, Å
Glc-I-O2	Q6-O	40.3	3.2
Gal’-II-O6	E159-Oε1	31.8	3.1
Glc-II-O3	N173-Oδ1	71.4	3.3
Glc-III-O6	V99-O^a	38.7	3.1
Glc-IV-O6	L96-O	33.0	3.2
Gal-V-O2	Y37-OH	67.9	3.4
Gal’-V-O2	D213-Oδ1	53.1	3.1
Neu5Ac-V-O4	G139-O	61.2	3.2
Neu5Ac-V-O4	Y145-OH	33.5	3.6
GlcNAc-II-C=O	G157-N	86.2	3.1
Glc-II-O3	N173-Nδ2	76.3	3.4
Gal-III-O4	A174-N	99.7	3.3
Neu5Ac-V-O1a	R210-NH1	90.1	2.8
Neu5Ac-V-O1b	R210-NH2	88.6	3.0
Gal’-V-O3	R210-NH2	65.1	3.6
Neu5Ac-V-O1b	Y214-OH	98.6	3.0
Glc-I-O3	Q6-N	31.4	3.6
Gal’-I-O6	L9-N	66.6	3.3
Neu5Ac-IV-O4	Y37-OH	53.7	3.2
GlcNAc-V-C=O	R55-NH1	53.0	2.9
Gal-IV-O6	V99-N	75.4	3.3
Ring stacking (LH)
CPS residue	Fv residue	θ, °	Distance
Glc-IV	Y37	156	5.9
Glc-V	Y145	152.5	5.4
Gal-V	Y212	148.3	6.3
GlcNAc-V	Y212	138.4	4.9

*Contacts involving residues in CDR loops are in boldface type.

Table 4. Predicted H-bond occupancies, distances, and ring stacking interactions between Fv 1B1 and the GBSIII CPS (H → L threading)

H-bond*
CPS Atom	Fv atom		Occupancy, %		Distance, Å
GlcNAc-I-O2	G139-O^a		75.2		3.0
GlcNAc-III-O6	H98-ND1		30.6		3.5
GlcNAc-IV-O6	N173-OD1		37.3		3.2
Gal-V-O2	D1-OD1		41.6		3.2
GlcNAc-V-N2	F103-O		57.0		3.4
Gal’-I-O6	Q114-N		33.6		3.4
Gal-I-O4	G139-N		30.0		3.4
GlcNAc-I-O2N	G139-N		44.6		3.1
Glc-IV-O6	A174-N		53.6		3.6
Gal-II-O6	R210-NH1		34.5		3.2
Glc-I-O3	R210-NH1		62.9		3.5
Glc-I-O3	R210-NH2		31.2		3.2
Gal-IV-O6	Q27-NE2		32.9		3.2
Glc-II-O2	R55-NH1		42.1		3.5
Glc-II-O3	R55-NH2		43.8		3.4
Glc-III-O6	V99-N		99.5		3.2
Ring Stacking (HL)
CPS residue		Fv residue		θ, °	Distance
Glc-I		Y145		135.2	6.7
GlcNAc-II		Y212		136.8	6.6

*Contacts involving residues in CDR loops are in boldface type.

Table 5. Predicted H-bond occupancies and distances observed in the MD simulation of the Fv1B1:GBSIII CPS complex

CPS atom	Fv atom	Occupancy, %	Distance, Å
Gal-I-O4	T5-Og1	86	3.3
Gal-II-O6	M4-O	33	3.4
Gal-II-O6	F103-O	34	3.6
Glc-II-O6	D1-Od1	47	3.2
Glc-II-O3	N173-Od1	29	3.4
Gal-III-O4	Y172-O	22	3.4
Glc-IV-O6	L96-O	36	3.5
Neu5Ac-IV-O4	Y37-OH	31	3.6
Gal'-V-O2	D213-Od1	56	3.7
Gal'-V-O2	D213-Od2	93	2.9
Neu5Ac-V-O4	Y145-OH	40	3.3
Gal'-V-O2	Y145-OH	27	3.3
Glc-II-O3	N173-Nd2	46	3.6
Gal-III-O4	A174-N	96	3.3
GlcNAc-I-O2N	T7-Og1	21	3.6
Gal-I-O	R24-Ne	22	3.5
Gal-I-O	R24-NH2	21	3.5
Neu5Ac-IV-O4	N35-Nd2	34	3.5
Neu5Ac-IV-O1A	N35-Nd2	83	2.9
Neu5Ac-IV-O1B	N35-Nd2	40	3.5
Neu5Ac-IV-O1A	R55-NH2	21	3.1
Neu5Ac-IV-O4	R55-NH2	58	3.2
Gal-III-O6	Y101-N	95	3.3

Contacts involving residues in CDR loops are in boldface type.

Table 6. Predicted H-bond occupancies and distances observed in the MD simulation
of the Fv1B1:Pn14 CPS complex

CPS atom	Fv atom	Occupancy, %	Distance, Å
Glc-I-O2	Q6-O	50	3.2
Gal-II-O6	F103-O	36	3.1
Glc-II-O3	N173-Od1	52	3.3
Glc-III-O6	V99-O	33	3.1
Gal-IV-O6	V99-O	24	3.4
Glc-IV-O6	L96-O	25	3.5
Gal-V-O2	Y37-OH	44	3.5
GlcNAc-V-N2	Y54-OH	58	3.4
Gal'-V-O2	D213-Od1	36	3.1
Gal'-V-O2	Y145-OH	32	3.3
GlcNAc-II-O2N	G157-N	36	3.1
Glc-II-O3	N173-Nd2	74	3.5
Gal-III-O4	A174-N	97	3.3
Gal'-V-O2	R210-NH2	26	3.4
Glc-IV-O6	W212-Ne1	35	3.5
Gal'-I-O6	L9-N	52	3.3
Gal-V-O2	Y54-OH	23	3.3
GlcNAc-V-O2N	Y54-OH	26	3.1
GlcNAc-V-O2N	R55-NH1	62	2.9

Contacts involving residues in CDR loops are in boldface type.